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Conserved domains on  [gi|578831745|ref|XP_006722277|]
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probable helicase with zinc finger domain isoform X1 [Homo sapiens]

Protein Classification

zinc finger CCCH domain-containing protein( domain architecture ID 13638697)

zinc finger CCCH domain-containing protein similar to Homo sapiens proline-rich protein 3 (PRR3)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 668-895 9.30e-152

DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. HELZ is a member of the family I class of RNA helicases of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


:

Pssm-ID: 350835 [Multi-domain]  Cd Length: 226  Bit Score: 466.58  E-value: 9.30e-152
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  668 RLNAKQKEAVLAITTPLAIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQETsRILICTHSNSAADLYIKDYLHPYVEAGN 747
Cdd:cd18077     1 RLNAKQKEAVLAITTPLSIQLPPVLLIGPFGTGKTFTLAQAVKHILQQPET-RILICTHSNSAADLYIKEYLHPYVETGN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  748 PQARPLRVYFRNRWVKTVHPVVHQYCLISsAHSTFQMPQKEDILKHRVVVVTLNTSQYLCQLDLEPGFFTHILLDEAAQA 827
Cdd:cd18077    80 PRARPLRVYYRNRWVKTVHPVVQKYCLID-EHGTFRMPTREDVMRHRVVVVTLSTSQYLCQLDLEPGFFTHILLDEAAQA 158

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 578831745  828 MECETIMPLALATQNTRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEHYPAEFPCRILLCENYR 895
Cdd:cd18077   159 MECEAIMPLALATKSTRIVLAGDHMQLSPEVYSEFARERNLHISLLERLYEHYPSEHPCRILLCENYR 226
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
793-1102 9.24e-42

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


:

Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 167.23  E-value: 9.24e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  793 HRVVVVTLNTSQYLcqLDLEPGFFTHILLDEAAQAMECETIMPLALATqntRIVLAGDHMQLSPFV---YSEFARERNLH 869
Cdd:COG1112   535 APVVGMTPASVARL--LPLGEGSFDLVIIDEASQATLAEALGALARAK---RVVLVGDPKQLPPVVfgeEAEEVAEEGLD 609

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  870 VSLLDRLYEHYPaefPCRILLCENYRSHEAIINYTSELFYEGKLMA---SGKQPAHKDFYPLTFFTARGedVQEKNSTAF 946
Cdd:COG1112   610 ESLLDRLLARLP---ERGVMLREHYRMHPEIIAFSNRLFYDGKLVPlpsPKARRLADPDSPLVFIDVDG--VYERRGGSR 684

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  947 YNnaevfevverveelrrkwP------VAW------GKLDDGSIGVVTPYADQVFRIRAELRKKRLSDV------NVERv 1008
Cdd:COG1112   685 TN------------------PeeaeavVELvrelleDGPDGESIGVITPYRAQVALIRELLREALGDGLepvfvgTVDR- 745

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745 1009 lnVQGKQFRVLFLSTVRTRhtckhkqtpikkkeqlleDSTEDLDYGFLS-NYKLLNTAITRAQSLVAVVGDPiALCSIGR 1087
Cdd:COG1112   746 --FQGDERDVIIFSLVYSN------------------DEDVPRNFGFLNgGPRRLNVAVSRARRKLIVVGSR-ELLDSDP 804

                         330
                  ....*....|....*
gi 578831745 1088 CRKFWERFIALCHEN 1102
Cdd:COG1112   805 STPALKRLLEYLERA 819
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
181-205 6.50e-06

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


:

Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 44.49  E-value: 6.50e-06
                           10        20
                   ....*....|....*....|....*
gi 578831745   181 YTLCKRFLEQGICRYGAQCTSAHSQ 205
Cdd:pfam00642    3 TELCRFFLRTGYCKYGDRCKFAHGQ 27
 
Name Accession Description Interval E-value
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 668-895 9.30e-152

DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. HELZ is a member of the family I class of RNA helicases of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350835 [Multi-domain]  Cd Length: 226  Bit Score: 466.58  E-value: 9.30e-152
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  668 RLNAKQKEAVLAITTPLAIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQETsRILICTHSNSAADLYIKDYLHPYVEAGN 747
Cdd:cd18077     1 RLNAKQKEAVLAITTPLSIQLPPVLLIGPFGTGKTFTLAQAVKHILQQPET-RILICTHSNSAADLYIKEYLHPYVETGN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  748 PQARPLRVYFRNRWVKTVHPVVHQYCLISsAHSTFQMPQKEDILKHRVVVVTLNTSQYLCQLDLEPGFFTHILLDEAAQA 827
Cdd:cd18077    80 PRARPLRVYYRNRWVKTVHPVVQKYCLID-EHGTFRMPTREDVMRHRVVVVTLSTSQYLCQLDLEPGFFTHILLDEAAQA 158

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 578831745  828 MECETIMPLALATQNTRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEHYPAEFPCRILLCENYR 895
Cdd:cd18077   159 MECEAIMPLALATKSTRIVLAGDHMQLSPEVYSEFARERNLHISLLERLYEHYPSEHPCRILLCENYR 226
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
793-1102 9.24e-42

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 167.23  E-value: 9.24e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  793 HRVVVVTLNTSQYLcqLDLEPGFFTHILLDEAAQAMECETIMPLALATqntRIVLAGDHMQLSPFV---YSEFARERNLH 869
Cdd:COG1112   535 APVVGMTPASVARL--LPLGEGSFDLVIIDEASQATLAEALGALARAK---RVVLVGDPKQLPPVVfgeEAEEVAEEGLD 609

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  870 VSLLDRLYEHYPaefPCRILLCENYRSHEAIINYTSELFYEGKLMA---SGKQPAHKDFYPLTFFTARGedVQEKNSTAF 946
Cdd:COG1112   610 ESLLDRLLARLP---ERGVMLREHYRMHPEIIAFSNRLFYDGKLVPlpsPKARRLADPDSPLVFIDVDG--VYERRGGSR 684

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  947 YNnaevfevverveelrrkwP------VAW------GKLDDGSIGVVTPYADQVFRIRAELRKKRLSDV------NVERv 1008
Cdd:COG1112   685 TN------------------PeeaeavVELvrelleDGPDGESIGVITPYRAQVALIRELLREALGDGLepvfvgTVDR- 745

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745 1009 lnVQGKQFRVLFLSTVRTRhtckhkqtpikkkeqlleDSTEDLDYGFLS-NYKLLNTAITRAQSLVAVVGDPiALCSIGR 1087
Cdd:COG1112   746 --FQGDERDVIIFSLVYSN------------------DEDVPRNFGFLNgGPRRLNVAVSRARRKLIVVGSR-ELLDSDP 804

                         330
                  ....*....|....*
gi 578831745 1088 CRKFWERFIALCHEN 1102
Cdd:COG1112   805 STPALKRLLEYLERA 819
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 896-1096 1.07e-35

C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350195 [Multi-domain]  Cd Length: 184  Bit Score: 134.67  E-value: 1.07e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  896 SHEAIINYTSELFYEGKLMAS-------GKQPAHKDFYPLTFFTARGEDVQEKNSTAFYNNAEVFEVVERVEELRRKWpv 968
Cdd:cd18808     1 MHPEISEFPSKLFYEGKLKAGvsvaarlNPPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKSG-- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  969 awgkLDDGSIGVVTPYADQVFRIRAELRKKR--LSDVNVERVLNVQGKQFRVLFLSTVRTRHTCKHkqtpikkkeqlled 1046
Cdd:cd18808    79 ----VKPSSIGVITPYRAQVALIRELLRKRGglLEDVEVGTVDNFQGREKDVIILSLVRSNESGGS-------------- 140

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 578831745 1047 stedldYGFLSNYKLLNTAITRAQSLVAVVGDPIALCSIGRCRKFWERFI 1096
Cdd:cd18808   141 ------IGFLSDPRRLNVALTRAKRGLIIVGNPDTLSKDPLWKKLLEYLE 184
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 868-1079 3.96e-35

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.


Pssm-ID: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 133.44  E-value: 3.96e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   868 LHVSLLDRLYEHYPAefpCRILLCENYRSHEAIINYTSELFYEGKLMASGKQPAH---------KDFYPLTFF-TARGED 937
Cdd:pfam13087    1 LDRSLFERLQELGPS---AVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERplpddfhlpDPLGPLVFIdVDGSEE 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   938 VQEKNSTAFYNNAEVFEVVERVEELRRKWPVAWGKlddgsIGVVTPYADQVFRIRAELRKKRLSDVNVErVLNV---QGK 1014
Cdd:pfam13087   78 EESDGGTSYSNEAEAELVVQLVEKLIKSGPEEPSD-----IGVITPYRAQVRLIRKLLKRKLGGKLEIE-VNTVdgfQGR 151

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 578831745  1015 QFRVLFLSTVRtrhtckhkqtpikkkeqlledSTEDLDYGFLSNYKLLNTAITRAQSLVAVVGDP 1079
Cdd:pfam13087  152 EKDVIIFSCVR---------------------SNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNA 195
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 673-861 1.51e-14

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.


Pssm-ID: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 75.46  E-value: 1.51e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   673 QKEAVLAittplAIQLPPV-LIIGPYGTGKTFTLAQAVKHILQQQETS-----RILICTHSNSAAD----LYIKDYLHPY 742
Cdd:pfam13086    2 QREAIRS-----ALSSSHFtLIQGPPGTGKTTTIVELIRQLLSYPATSaaagpRILVCAPSNAAVDnileRLLRKGQKYG 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   743 VEA---GNPQARplrvyfrnrwvktvHPVVHQYCLISSAHSTFQMPQKEDILK--------------------------- 792
Cdd:pfam13086   77 PKIvriGHPAAI--------------SEAVLPVSLDYLVESKLNNEEDAQIVKdiskeleklakalrafekeiivekllk 142

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   793 -----------------------------------------HRVVVVTLNTS--QYLCQLDlepGFFThILLDEAAQAME 829
Cdd:pfam13086  143 srnkdkskleqerrklrserkelrkelrrreqslereildeAQIVCSTLSGAgsRLLSSLA---NFDV-VIIDEAAQALE 218

                          250       260       270
                   ....*....|....*....|....*....|..
gi 578831745   830 CETIMPLALATqnTRIVLAGDHMQLSPFVYSE 861
Cdd:pfam13086  219 PSTLIPLLRGP--KKVVLVGDPKQLPPTVISK 248
UvrD COG0210
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
668-731 2.01e-06

Superfamily I DNA or RNA helicase [Replication, recombination and repair];


Pssm-ID: 439980 [Multi-domain]  Cd Length: 721  Bit Score: 53.02  E-value: 2.01e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 578831745  668 RLNAKQKEAVLAITTPLaiqlppvLII-GPyGTGKTFTLAQAVKHILQQQETS--RILICTHSNSAA 731
Cdd:COG0210     6 GLNPEQRAAVEHPEGPL-------LVLaGA-GSGKTRVLTHRIAYLIAEGGVDpeQILAVTFTNKAA 64
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
181-205 6.50e-06

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 44.49  E-value: 6.50e-06
                           10        20
                   ....*....|....*....|....*
gi 578831745   181 YTLCKRFLEQGICRYGAQCTSAHSQ 205
Cdd:pfam00642    3 TELCRFFLRTGYCKYGDRCKFAHGQ 27
 
Name Accession Description Interval E-value
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 668-895 9.30e-152

DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. HELZ is a member of the family I class of RNA helicases of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350835 [Multi-domain]  Cd Length: 226  Bit Score: 466.58  E-value: 9.30e-152
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  668 RLNAKQKEAVLAITTPLAIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQETsRILICTHSNSAADLYIKDYLHPYVEAGN 747
Cdd:cd18077     1 RLNAKQKEAVLAITTPLSIQLPPVLLIGPFGTGKTFTLAQAVKHILQQPET-RILICTHSNSAADLYIKEYLHPYVETGN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  748 PQARPLRVYFRNRWVKTVHPVVHQYCLISsAHSTFQMPQKEDILKHRVVVVTLNTSQYLCQLDLEPGFFTHILLDEAAQA 827
Cdd:cd18077    80 PRARPLRVYYRNRWVKTVHPVVQKYCLID-EHGTFRMPTREDVMRHRVVVVTLSTSQYLCQLDLEPGFFTHILLDEAAQA 158

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 578831745  828 MECETIMPLALATQNTRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEHYPAEFPCRILLCENYR 895
Cdd:cd18077   159 MECEAIMPLALATKSTRIVLAGDHMQLSPEVYSEFARERNLHISLLERLYEHYPSEHPCRILLCENYR 226
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 668-895 7.09e-95

DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350796 [Multi-domain]  Cd Length: 229  Bit Score: 306.08  E-value: 7.09e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  668 RLNAKQKEAVLAITTPlAIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQETSRILICTHSNSAADLYIKDYLHPYVeagn 747
Cdd:cd18038     1 ELNDEQKLAVRNIVTG-TSRPPPYIIFGPPGTGKTVTLVEAILQVLRQPPEARILVCAPSNSAADLLAERLLNALV---- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  748 PQARPLRVYFRNRWVKTVHPVVHQYClISSAHSTFQMPQKEDILKHRVVVVTLNTSQYLCQLDLEPGFFTHILLDEAAQA 827
Cdd:cd18038    76 TKREILRLNAPSRDRASVPPELLPYC-NSKAEGTFRLPSLEELKKYRIVVCTLMTAGRLVQAGVPNGHFTHIFIDEAGQA 154

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 578831745  828 MECETIMPLA-LATQNTRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEHYP------AEFPCRILLCENYR 895
Cdd:cd18038   155 TEPEALIPLSeLASKNTQIVLAGDPKQLGPVVRSPLARKYGLGKSLLERLMERPLyykdgeYNPSYITKLLKNYR 229
DEXXQc_HELZ2-N cd18076
N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 668-895 9.77e-68

N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB, and RXRA. It belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350834 [Multi-domain]  Cd Length: 230  Bit Score: 228.62  E-value: 9.77e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  668 RLNAKQKEAVLAIT--TPLAIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQETsRILICTHSNSAADLYIKDYLHPYVEA 745
Cdd:cd18076     1 AGNNKQQLAFNFIAgkPSEARFVPPLLIYGPFGTGKTFTLAMAALEVIREPGT-KVLICTHTNSAADIYIREYFHPYVDK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  746 GNPQARPLRVYFRNRWVKTVHPVVHQYCLISSAHSTFQMPQKEDILKHRVVVVTLNTSQylcQLDLEPGFFTHILLDEAA 825
Cdd:cd18076    80 GHPEARPLRIKATDRPNAITDPDTITYCCLTKDRQCFRLPTRDELDFHNIVITTTAMAF---NLHVLSGFFTHIFIDEAA 156

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 578831745  826 QAMECETIMPLALATQNTRIVLAGDHMQLSPFVYSeFARERNLHVSLLDRLYEHYPAE-----FPCRILLCENYR 895
Cdd:cd18076   157 QMLECEALIPLSYAGPKTRVVLAGDHMQMTPKLFS-VADYNRANHTLLNRLFHYYQGEkhevaVKSRVIFSENYR 230
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
793-1102 9.24e-42

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 167.23  E-value: 9.24e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  793 HRVVVVTLNTSQYLcqLDLEPGFFTHILLDEAAQAMECETIMPLALATqntRIVLAGDHMQLSPFV---YSEFARERNLH 869
Cdd:COG1112   535 APVVGMTPASVARL--LPLGEGSFDLVIIDEASQATLAEALGALARAK---RVVLVGDPKQLPPVVfgeEAEEVAEEGLD 609

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  870 VSLLDRLYEHYPaefPCRILLCENYRSHEAIINYTSELFYEGKLMA---SGKQPAHKDFYPLTFFTARGedVQEKNSTAF 946
Cdd:COG1112   610 ESLLDRLLARLP---ERGVMLREHYRMHPEIIAFSNRLFYDGKLVPlpsPKARRLADPDSPLVFIDVDG--VYERRGGSR 684

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  947 YNnaevfevverveelrrkwP------VAW------GKLDDGSIGVVTPYADQVFRIRAELRKKRLSDV------NVERv 1008
Cdd:COG1112   685 TN------------------PeeaeavVELvrelleDGPDGESIGVITPYRAQVALIRELLREALGDGLepvfvgTVDR- 745

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745 1009 lnVQGKQFRVLFLSTVRTRhtckhkqtpikkkeqlleDSTEDLDYGFLS-NYKLLNTAITRAQSLVAVVGDPiALCSIGR 1087
Cdd:COG1112   746 --FQGDERDVIIFSLVYSN------------------DEDVPRNFGFLNgGPRRLNVAVSRARRKLIVVGSR-ELLDSDP 804

                         330
                  ....*....|....*
gi 578831745 1088 CRKFWERFIALCHEN 1102
Cdd:COG1112   805 STPALKRLLEYLERA 819
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
 669-895 3.95e-40

DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. Mov10L1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350836 [Multi-domain]  Cd Length: 230  Bit Score: 149.06  E-value: 3.95e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  669 LNAKQKEAVLAITTPLAIQLPPVlIIGPYGTGKTFTLAQAVKHILQQQETSRILICTHSNSAADLYIKDyLHPYVEAGNP 748
Cdd:cd18078     2 LNELQKEAVKRILGGECRPLPYI-LFGPPGTGKTVTIIEAILQVVYNLPRSRILVCAPSNSAADLVTSR-LHESKVLKPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  749 QARPLRVYfrNRWVKTVHPVVHQYCLISSahstfqmpQKEDILKHRVVVVTLNTSQYLCQLDLEPGFFTHILLDEAAQAM 828
Cdd:cd18078    80 DMVRLNAV--NRFESTVIDARKLYCRLGE--------DLSKASRHRIVISTCSTAGLLYQMGLPVGHFTHVFVDEAGQAT 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  829 ECETIMPLALATQNT-RIVLAGDHMQLSPFVYSEFARERNLHVSLLDRL-----YEHYPAEFP-CRIL-------LCENY 894
Cdd:cd18078   150 EPESLIPLGLISSRDgQIILAGDPMQLGPVIKSRLASAYGLGVSFLERLmnrplYLRDPNRFGeSGGYnpllvtkLVDNY 229


                  .
gi 578831745  895 R 895
Cdd:cd18078   230 R 230
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 896-1096 1.07e-35

C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350195 [Multi-domain]  Cd Length: 184  Bit Score: 134.67  E-value: 1.07e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  896 SHEAIINYTSELFYEGKLMAS-------GKQPAHKDFYPLTFFTARGEDVQEKNSTAFYNNAEVFEVVERVEELRRKWpv 968
Cdd:cd18808     1 MHPEISEFPSKLFYEGKLKAGvsvaarlNPPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKSG-- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  969 awgkLDDGSIGVVTPYADQVFRIRAELRKKR--LSDVNVERVLNVQGKQFRVLFLSTVRTRHTCKHkqtpikkkeqlled 1046
Cdd:cd18808    79 ----VKPSSIGVITPYRAQVALIRELLRKRGglLEDVEVGTVDNFQGREKDVIILSLVRSNESGGS-------------- 140

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 578831745 1047 stedldYGFLSNYKLLNTAITRAQSLVAVVGDPIALCSIGRCRKFWERFI 1096
Cdd:cd18808   141 ------IGFLSDPRRLNVALTRAKRGLIIVGNPDTLSKDPLWKKLLEYLE 184
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 868-1079 3.96e-35

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.


Pssm-ID: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 133.44  E-value: 3.96e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   868 LHVSLLDRLYEHYPAefpCRILLCENYRSHEAIINYTSELFYEGKLMASGKQPAH---------KDFYPLTFF-TARGED 937
Cdd:pfam13087    1 LDRSLFERLQELGPS---AVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERplpddfhlpDPLGPLVFIdVDGSEE 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   938 VQEKNSTAFYNNAEVFEVVERVEELRRKWPVAWGKlddgsIGVVTPYADQVFRIRAELRKKRLSDVNVErVLNV---QGK 1014
Cdd:pfam13087   78 EESDGGTSYSNEAEAELVVQLVEKLIKSGPEEPSD-----IGVITPYRAQVRLIRKLLKRKLGGKLEIE-VNTVdgfQGR 151

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 578831745  1015 QFRVLFLSTVRtrhtckhkqtpikkkeqlledSTEDLDYGFLSNYKLLNTAITRAQSLVAVVGDP 1079
Cdd:pfam13087  152 EKDVIIFSCVR---------------------SNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNA 195
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 668-881 2.49e-25

DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350799 [Multi-domain]  Cd Length: 203  Bit Score: 105.40  E-value: 2.49e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  668 RLNAKQKEAVLAITTPLAIqlppVLIIGPYGTGKTFTLAQAVKhILQQQETSrILICTHSNSAAD---LYIKDYLHPYVE 744
Cdd:cd18041     1 GLNKDQRQAIKKVLNAKDY----ALILGMPGTGKTTTIAALVR-ILVALGKS-VLLTSYTHSAVDnilLKLKKFGVNFLR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  745 AGNPqarplrvyfrnrwvKTVHPVVHQYCLISSAHSTFQMPQKEDIL-KHRVVVVTL--NTSQYLCQldlepGFFTHILL 821
Cdd:cd18041    75 LGRL--------------KKIHPDVQEFTLEAILKSCKSVEELESKYeSVSVVATTClgINHPIFRR-----RTFDYCIV 135

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  822 DEAAQAMECETIMPLALATqntRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEHYP 881
Cdd:cd18041   136 DEASQITLPICLGPLRLAK---KFVLVGDHYQLPPLVKSREARELGMDESLFKRLSEAHP 192
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 668-895 3.93e-25

DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350802 [Multi-domain]  Cd Length: 191  Bit Score: 104.61  E-value: 3.93e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  668 RLNAKQKEAVLaittpLAIQLPPVLII-GPYGTGKTFTLAQAVKHILQQQEtsRILICTHSNSAADLYIKDYLH---PYV 743
Cdd:cd18044     1 NLNDSQKEAVK-----FALSQKDVALIhGPPGTGKTTTVVEIILQAVKRGE--KVLACAPSNIAVDNLVERLVAlkvKVV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  744 EAGNPqARplrvyfrnrwvktVHPVVHQYCLissahstfqmpqkEDILKHRVVVVTLNTSqylCQLDLEPG-FFTHILLD 822
Cdd:cd18044    74 RIGHP-AR-------------LLESVLDHSL-------------DALVAAQVVLATNTGA---GSRQLLPNeLFDVVVID 123

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 578831745  823 EAAQAMECETIMPLALATqntRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEHYPAEfpCRILLCENYR 895
Cdd:cd18044   124 EAAQALEASCWIPLLKAR---RCILAGDHKQLPPTILSDKAARGGLGVTLFERLVNLYGES--VVRMLTVQYR 191
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 669-876 1.67e-19

DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350797 [Multi-domain]  Cd Length: 234  Bit Score: 89.61  E-value: 1.67e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  669 LNAKQKEAVLAittplAIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQEtSRILICTHSNSAADlYIKDYLHpyvEAGnp 748
Cdd:cd18039     2 LNHSQVDAVKT-----ALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGN-GPVLVCAPSNVAVD-QLTEKIH---QTG-- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  749 qARPLRVYFRNRW-----VK--TVHPVVHQY-----------------CLISSAHSTFQM----PQKEDILKHRVVVVTL 800
Cdd:cd18039    70 -LKVVRLCAKSREavespVSflALHNQVRNLdsaeklellkllkletgELSSADEKRYRKlkrkAERELLRNADVICCTC 148

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 578831745  801 NTSqylcqLD--LEPGFFTHILLDEAAQAMECETIMPLALATQntRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRL 876
Cdd:cd18039   149 VGA-----GDprLSKMKFRTVLIDEATQATEPECLIPLVHGAK--QVILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 219
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 669-895 5.04e-19

DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438712 [Multi-domain]  Cd Length: 218  Bit Score: 87.65  E-value: 5.04e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  669 LNAKQKEAVLAIttpLAIQLPPVLIIGPYGTGKTFTL---------------AQAVKHILQQQETS--------RILICT 725
Cdd:cd18042     1 LNESQLEAIASA---LQNSPGITLIQGPPGTGKTKTIvgilsvllagkyrkyYEKVKKKLRKLQRNlnnkkkknRILVCA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  726 HSNSAADLYIKDYLHPYVEAGNPQARPLRVyfrnrwVKTVHpvvhqyclissahstfQMPQKEDILKHRVVVVTLNTSQY 805
Cdd:cd18042    78 PSNAAVDEIVLRLLSEGFLDGDGRSYKPNV------VRVGR----------------QELRASILNEADIVCTTLSSSGS 135

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  806 LcQLDLEPGFFTHILLDEAAQAMECETIMPLALATQntRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEhypAEFP 885
Cdd:cd18042   136 D-LLESLPRGFDTVIIDEAAQAVELSTLIPLRLGCK--RLILVGDPKQLPATVFSKVAQKLGYDRSLFERLQL---AGYP 209

                         250
                  ....*....|
gi 578831745  886 CrILLCENYR 895
Cdd:cd18042   210 V-LMLTTQYR 218
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 668-876 4.25e-16

EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350694 [Multi-domain]  Cd Length: 178  Bit Score: 77.97  E-value: 4.25e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  668 RLNAKQKEA-VLAITTPLAIqlppvlIIGPYGTGKTFTLAQAVKHILQ---QQETSRILICTHSNSAADLYIKDYLhpyv 743
Cdd:cd17936     1 TLDPSQLEAlKHALTSELAL------IQGPPGTGKTFLGVKLVRALLQnqdLSITGPILVVCYTNHALDQFLEGLL---- 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  744 EAGNPQArpLRVYFRnrwvktvhpVVHqyCLISSAHSTFQMPQKediLKHRVVVVtlntsqylcqldlepgffthillDE 823
Cdd:cd17936    71 DFGPTKI--VRLGAR---------VIG--MTTTGAAKYRELLQA---LGPKVVIV-----------------------EE 111

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 578831745  824 AAQAMECETIMPLalaTQNTR-IVLAGDHMQLSPFV--YSEFARERNLHVSLLDRL 876
Cdd:cd17936   112 AAEVLEAHILAAL---TPSTEhLILIGDHKQLRPKVnvYELTAKKYNLDVSLFERL 164
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 691-895 1.80e-15

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 74.58  E-value: 1.80e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  691 VLIIGPYGTGKTFTLAQAVKHILQQQETSRILICTHSNSAADlyikdylhpyveagnpqarplrvyfrnrwvktvhpvvh 770
Cdd:cd17934     2 SLIQGPPGTGKTTTIAAIVLQLLKGLRGKRVLVTAQSNVAVD-------------------------------------- 43

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  771 qyclissahstfqmpqkedilkhrvvvvtlntsqylcQLDlepgfftHILLDEAAQAMECETIMPLALAtqnTRIVLAGD 850
Cdd:cd17934    44 -------------------------------------NVD-------VVIIDEASQITEPELLIALIRA---KKVVLVGD 76

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 578831745  851 HMQLSPFVYSEFARE--RNLHVSLLDRLYEHYPAEFPcrILLCENYR 895
Cdd:cd17934    77 PKQLPPVVQEDHAALlgLSFILSLLLLFRLLLPGSPK--VMLDTQYR 121
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 673-861 1.51e-14

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.


Pssm-ID: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 75.46  E-value: 1.51e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   673 QKEAVLAittplAIQLPPV-LIIGPYGTGKTFTLAQAVKHILQQQETS-----RILICTHSNSAAD----LYIKDYLHPY 742
Cdd:pfam13086    2 QREAIRS-----ALSSSHFtLIQGPPGTGKTTTIVELIRQLLSYPATSaaagpRILVCAPSNAAVDnileRLLRKGQKYG 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   743 VEA---GNPQARplrvyfrnrwvktvHPVVHQYCLISSAHSTFQMPQKEDILK--------------------------- 792
Cdd:pfam13086   77 PKIvriGHPAAI--------------SEAVLPVSLDYLVESKLNNEEDAQIVKdiskeleklakalrafekeiivekllk 142

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   793 -----------------------------------------HRVVVVTLNTS--QYLCQLDlepGFFThILLDEAAQAME 829
Cdd:pfam13086  143 srnkdkskleqerrklrserkelrkelrrreqslereildeAQIVCSTLSGAgsRLLSSLA---NFDV-VIIDEAAQALE 218

                          250       260       270
                   ....*....|....*....|....*....|..
gi 578831745   830 CETIMPLALATqnTRIVLAGDHMQLSPFVYSE 861
Cdd:pfam13086  219 PSTLIPLLRGP--KKVVLVGDPKQLPPTVISK 248
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 669-878 1.93e-12

C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB and RXRA. It belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350798 [Multi-domain]  Cd Length: 271  Bit Score: 69.86  E-value: 1.93e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  669 LNAKQKEAVL-AITTPLaiqlppVLIIGPYGTGKTFTLAQAVKHILQQQETSR-----------ILICTHSNSAADLyIK 736
Cdd:cd18040     2 LNPSQNHAVRtALTKPF------TLIQGPPGTGKTVTGVHIAYWFAKQNREIQsvsgegdggpcVLYCGPSNKSVDV-VA 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  737 DYLhpyveAGNPQARPLRVY--------------FRNRWVK--------------TVHPVVHQ----YC-LISSAHSTFQ 783
Cdd:cd18040    75 ELL-----LKVPGLKILRVYseqietteypipnePRHPNKKsereskpnselssiTLHHRIRQpsnpHSqQIKAFEARFE 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  784 MPQ----KEDILKHRVVV------------VTLNTsqylCQLDLEPGFFTH-----ILLDEAAQAMECETIMPLALATQN 842
Cdd:cd18040   150 RTQekitEEDIKTYKILIwearfeeletvdVILCT----CSEAASQKMRTHanvkqCIVDECGMCTEPESLIPIVSAPRA 225

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 578831745  843 TRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYE 878
Cdd:cd18040   226 EQVVLIGDHKQLRPVVQNKEAQKLGLGRSLFERYAE 261
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
 668-876 4.31e-11

EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds precursor-mRNA introns at a defined position and is part of a pentameric intron-binding complex (IBC). It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350693 [Multi-domain]  Cd Length: 207  Bit Score: 64.37  E-value: 4.31e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  668 RLNAKQKEAVLAittplAIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQETSRILICTHSNSAA-DLYIKdylhpyVEAg 746
Cdd:cd17935     5 KFTPTQIEAIRS-----GMQPGLTMVVGPPGTGKTDVAVQIISNLYHNFPNQRTLIVTHSNQALnQLFEK------IMA- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  747 npqarpLRVYFRNrwvktvhpvvhqycLISSAHSTfqmpqkedilkhRVVVVTLnTSQYLCQLDL-EPGF-FTHILLDEA 824
Cdd:cd17935    73 ------LDIDERH--------------LLRLGHGA------------KIIAMTC-THAALKRGELvELGFkYDNILMEEA 119

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 578831745  825 AQAMECETIMPLALATQNT------RIVLAGDHMQLSPFVYS-EFARERNLHVSLLDRL 876
Cdd:cd17935   120 AQILEIETFIPLLLQNPEDgpnrlkRLIMIGDHHQLPPVIKNmAFQKYSNMEQSLFTRL 178
DEXQc_UvrD cd17932
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ...
 670-894 1.44e-08

DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350690 [Multi-domain]  Cd Length: 189  Bit Score: 56.37  E-value: 1.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  670 NAKQKEAVLAITTPLaiqlppvLII-GPyGTGKTFTLAQAVKHILQQQET--SRILICTHSNSAADlYIKDYLHPYVeaG 746
Cdd:cd17932     1 NPEQREAVTHPDGPL-------LVLaGA-GSGKTRVLTHRIAYLILEGGVppERILAVTFTNKAAK-EMRERLRKLL--G 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  747 NPQARPLrvyfrnrWVKTVHPVvhqyCL-ISSAHSTFqmpqkEDILkHRVVVVtLNTSQYLCQLDLEPgfFTHILLDEA- 824
Cdd:cd17932    70 EQLASGV-------WIGTFHSF----ALrILRRYGDF-----DDLL-LYALEL-LEENPDVREKLQSR--FRYILVDEYq 129

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 578831745  825 ----AQamecETIMpLALATQNTRIVLAGDHMQlSpfVYSeFareRNLHVSLLDRLYEHYPAefPCRILLCENY 894
Cdd:cd17932   130 dtnpLQ----YELL-KLLAGDGKNLFVVGDDDQ-S--IYG-F---RGADPENILDFEKDFPD--AKVIKLEENY 189
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 670-859 1.06e-07

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350801 [Multi-domain]  Cd Length: 127  Bit Score: 52.58  E-value: 1.06e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  670 NAKQKEAVLAittplAIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQEtsRILICTHSNSAADlyikdylhpyveagnpq 749
Cdd:cd18043     1 DSSQEAAIIS-----ARNGKNVVIQGPPGTGKSQTIANIIANALARGK--RVLFVSEKKAALD----------------- 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  750 arplrvyfrnrwvktvhpVVHQYCLISSAHSTFQMpqkedilkhrvvvvtlntsqylcqLDLEPGFFTHILLDEAAQAME 829
Cdd:cd18043    57 ------------------VVRFPCWIMSPLSVSQY------------------------LPLNRNLFDLVIFDEASQIPI 94

                         170       180       190
                  ....*....|....*....|....*....|
gi 578831745  830 CETIMPLALATQntrIVLAGDHMQLSPFVY 859
Cdd:cd18043    95 EEALPALFRGKQ---VVVVGDDKQLPPSIL 121
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 690-732 3.06e-07

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. Their helicase core is surrounded by C and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains or domains engaged in protein-protein interactions. SF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 50.95  E-value: 3.06e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 578831745  690 PVLIIGPYGTGKTFTLAQAVKHILQQQETS--RILICTHSNSAAD 732
Cdd:cd17914     1 LSLIQGPPGTGKTRVLVKIVAALMQNKNGEpgRILLVTPTNKAAA 45
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 672-856 1.96e-06

DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350691 [Multi-domain]  Cd Length: 155  Bit Score: 49.48  E-value: 1.96e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  672 KQKEAVLAITtplaiQLPPVLIIGPYGTGKTFTLAQAVKHIlqQQETSRILICTHSNSAADLyikdyLHpyvEAGNPQAR 751
Cdd:cd17933     1 EQKAAVRLVL-----RNRVSVLTGGAGTGKTTTLKALLAAL--EAEGKRVVLAAPTGKAAKR-----LS---ESTGIEAS 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  752 plrvyfrnrwvkTVHPVvhqycLISSAHSTFQMPQKEDILKHRVVVVtlntsqylcqldlepgffthillDEAaqAMece 831
Cdd:cd17933    66 ------------TIHRL-----LGINPGGGGFYYNEENPLDADLLIV-----------------------DEA--SM--- 100

                         170       180       190
                  ....*....|....*....|....*....|..
gi 578831745  832 tiMPLALATQ-------NTRIVLAGDHMQLSP 856
Cdd:cd17933   101 --VDTRLMAAllsaipaGARLILVGDPDQLPS 130
UvrD COG0210
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
668-731 2.01e-06

Superfamily I DNA or RNA helicase [Replication, recombination and repair];


Pssm-ID: 439980 [Multi-domain]  Cd Length: 721  Bit Score: 53.02  E-value: 2.01e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 578831745  668 RLNAKQKEAVLAITTPLaiqlppvLII-GPyGTGKTFTLAQAVKHILQQQETS--RILICTHSNSAA 731
Cdd:COG0210     6 GLNPEQRAAVEHPEGPL-------LVLaGA-GSGKTRVLTHRIAYLIAEGGVDpeQILAVTFTNKAA 64
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
181-205 6.50e-06

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 44.49  E-value: 6.50e-06
                           10        20
                   ....*....|....*....|....*
gi 578831745   181 YTLCKRFLEQGICRYGAQCTSAHSQ 205
Cdd:pfam00642    3 TELCRFFLRTGYCKYGDRCKFAHGQ 27
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 659-1100 7.65e-06

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 50.75  E-value: 7.65e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  659 RQWDEQLDPRLNAKQKEAVLAITTPLAIqlppVLIIGPYGTGKTFTLAQAVKHILQQQEtsRILICTHSNSAAD-LYikd 737
Cdd:COG0507   115 AALEPRAGITLSDEQREAVALALTTRRV----SVLTGGAGTGKTTTLRALLAALEALGL--RVALAAPTGKAAKrLS--- 185

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  738 ylhpyvEAGNPQARplrvyfrnrwvkTVHPVVHqyclISSAHSTFQMPQKEDILKHRVVVVtlntsqylcqldlepgfft 817
Cdd:COG0507   186 ------ESTGIEAR------------TIHRLLG----LRPDSGRFRHNRDNPLTPADLLVV------------------- 224

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  818 hillDEA--------AQAMEcetimplALATQNTRIVLAGDHMQLSP----FVYSEFARERNLHVSLLDrlyehypaefp 885
Cdd:COG0507   225 ----DEAsmvdtrlmAALLE-------ALPRAGARLILVGDPDQLPSvgagAVLRDLIESGTVPVVELT----------- 282

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  886 crillcENYRSHEAI-INYTSELFYEGKlMASGKQPAHKDFYPL----------------TFFTARGEDVQ-----EKnS 943
Cdd:COG0507   283 ------EVYRQADDSrIIELAHAIREGD-APEALNARYADVVFVeaedaeeaaeaivelyADRPAGGEDIQvlaptNA-G 354

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  944 TAFYN-------NAEVFEVVERVEELRRKW----PV-------AWGkLDDGSIGVVTPYADQVFRIRAELRKKRLSDVNV 1005
Cdd:COG0507   355 VDALNqairealNPAGELERELAEDGELELyvgdRVmftrndyDLG-VFNGDIGTVLSIDEDEGRLTVRFDGREIVTYDP 433

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745 1006 ERVLNV-----------QGKQF-RVLFLSTvrtrhtckhkqtpikkkeqlledsteDLDYGFLSNyKLLNTAITRAQSLV 1073
Cdd:COG0507   434 SELDQLelayaitvhksQGSTFdRVILVLP--------------------------SEHSPLLSR-ELLYTALTRARELL 486

                         490       500
                  ....*....|....*....|....*..
gi 578831745 1074 AVVGDPIALCSIgrCRKFWERFIALCH 1100
Cdd:COG0507   487 TLVGDRDALARA--VRRDTARATGLAE 511
UvrD-helicase pfam00580
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ...
 669-766 1.03e-05

UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyze ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.


Pssm-ID: 395462 [Multi-domain]  Cd Length: 267  Bit Score: 49.17  E-value: 1.03e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   669 LNAKQKEAVLAITTPLaiqlppvLIIGPYGTGKTFTLAQAVKHILQQQETS--RILICTHSNSAAD---LYIKDYLhpyv 743
Cdd:pfam00580    1 LNPEQRKAVTHLGGPL-------LVLAGAGSGKTRVLTERIAYLILEGGIDpeEILAVTFTNKAARemkERILKLL---- 69

                           90       100
                   ....*....|....*....|...
gi 578831745   744 eaGNPQARPLrvyfrnrWVKTVH 766
Cdd:pfam00580   70 --GKAELSEL-------NISTFH 83
ResIII pfam04851
Type III restriction enzyme, res subunit;
669-824 4.93e-05

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 45.74  E-value: 4.93e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   669 LNAKQKEAVLAITTPLAIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQETSRILICTHSNsaaDLY------IKDYLHPY 742
Cdd:pfam04851    4 LRPYQIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRK---DLLeqaleeFKKFLPNY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   743 VEAGNpqarPLRVYFRNRWVKTVHPVVhqyclissahSTFQmpqkedilkhrvvvvTLNTSQYLCQLDLEPGFFTHILLD 822
Cdd:pfam04851   81 VEIGE----IISGDKKDESVDDNKIVV----------TTIQ---------------SLYKALELASLELLPDFFDVIIID 131


                   ..
gi 578831745   823 EA 824
Cdd:pfam04851  132 EA 133
AAA_19 pfam13245
AAA domain;
673-732 7.28e-05

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 44.52  E-value: 7.28e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 578831745   673 QKEAVLAittplAIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQETS-RILICTHSNSAAD 732
Cdd:pfam13245    1 QREAVRT-----ALPSKVVLLTGGPGTGKTTTIRHIVALLVALGGVSfPILLAAPTGRAAK 56
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 668-856 1.19e-04

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.


Pssm-ID: 433343 [Multi-domain]  Cd Length: 191  Bit Score: 44.86  E-value: 1.19e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   668 RLNAKQKEAVLAITT-PLAIQLppvlIIGPYGTGKTFTLAQAVKHIlqQQETSRILICTHSNSAADLYIKDYLHPyveag 746
Cdd:pfam13604    1 TLNAEQAAAVRALLTsGDRVAV----LVGPAGTGKTTALKALREAW--EAAGYRVIGLAPTGRAAKVLGEELGIP----- 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745   747 npqARplrvyfrnrwvkTVHPVVHQYclissahstfqmPQKEDILKHRVVVVtlntsqylcqldlepgffthillDEAAQ 826
Cdd:pfam13604   70 ---AD------------TIAKLLHRL------------GGRAGLDPGTLLIV-----------------------DEAGM 99

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 578831745   827 A----MEcetiMPLALATQ-NTRIVLAGDHMQLSP 856
Cdd:pfam13604  100 VgtrqMA----RLLKLAEDaGARVILVGDPRQLPS 130
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
664-757 1.22e-03

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 43.86  E-value: 1.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578831745  664 QLDPRLNAKQKEAVLAITTPLAIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQetsRILICTHS----NSAADLyIKDYL 739
Cdd:COG1061    76 GTSFELRPYQQEALEALLAALERGGGRGLVVAPTGTGKTVLALALAAELLRGK---RVLVLVPRrellEQWAEE-LRRFL 151

                          90
                  ....*....|....*...
gi 578831745  740 HPYVEAGNPQARPLRVYF 757
Cdd:COG1061   152 GDPLAGGGKKDSDAPITV 169
AAA_22 pfam13401
AAA domain;
691-736 4.88e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 39.25  E-value: 4.88e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 578831745   691 VLIIGPYGTGKTfTLAQAVKHILQQQETSRILI-CTHSNSAADLYIK 736
Cdd:pfam13401    8 LVLTGESGTGKT-TLLRRLLEQLPEVRDSVVFVdLPSGTSPKDLLRA 53
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 673-729 7.90e-03

DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350790 [Multi-domain]  Cd Length: 163  Bit Score: 39.08  E-value: 7.90e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 578831745  673 QKEAVLAITTPLAIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQETSRILICTHSNS 729
Cdd:cd18032     5 QQEAIEALEEAREKGQRRALLVMATGTGKTYTAAFLIKRLLEANRKKRILFLAHREE 61
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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